Merge branch 'master' of github.com:minoda-lab/universc (3ec5ab14) · Commits · github_fork / Universc

launch_universc.sh

+14 −13

Original line number	Diff line number	Diff line
		@@ -2957,10 +2957,10 @@ else
		#remove phase blocks and linkers
		sed -E '
		/.*(.{9})ACTGGCCTGCGA(.{9})GGTAGCGGTGACA(.{9})(.{8})/ {
		s/.*(.{9})ACTGGCCTGCGA(.{9})GGTAGCGGTGACA(.{9})(.{8})/\1.2.4\4/g
		s/.*(.{9})ACTGGCCTGCGA(.{9})GGTAGCGGTGACA(.{9})(.{8})/\1\2\3\4/g
		n
		n
		s/.*(.{6}).{12}(.{6}).{13}(.{6})(.{8})/\1.2.4\4/g
		s/.*(.{6}).{12}(.{6}).{13}(.{6})(.{8})/\1\2\3\4/g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		done
		@@ -3106,6 +3106,7 @@ else
		n
		n
		s/^(.{10})(.{10})(.{10})(.{3})/\1\2\4//g
		s/^(.{10})(.{10})(.{10})(.{3})/\1\2\4/g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		sed -E '
		@@ -3113,7 +3114,7 @@ else
		s/^(.{10})(.{10})TGTGAGAAAGGG/\1\2GGG/g
		n
		n
		s/(.{10})(.{10})(.{9})(.{3})/\1\2\4//g
		s/(.{10})(.{10})(.{9})(.{3})/\1\2\4/g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		#convert TSO to expected length for 10x 5' (TSS in R1 from base 39)
		@@ -3152,10 +3153,10 @@ else
		#remove adapter if present
		sed -E '
		/^.(.{8})GA.................CTT(.{8})(.{6}).$/ {
		s/^.(.{8})GA.................CTT(.{8})(.{6}).$/\1.2.4/g
		s/^.(.{8})GA.................CTT(.{8})(.{6}).$/\1\2\3/g
		n
		n
		s/^(.{8}).{22}(.{8})(.{6}).*/\1.2.4/g
		s/^(.{8}).{22}(.{8})(.{6}).*/\1\2\3/g
		}' $convFile > ${crIN}/.temp
		#remove linker between barcode and UMI
		echo " ... barcode and UMI linker removed for ${technology}"
		@@ -3201,10 +3202,10 @@ else
		#remove phase blocks and linkers
		sed -E '
		/.*(.{6})CGACTCACTACAGGG(.{6})TCGGTGACACGATCG(.{6})(.{6})/ {
		s/.*(.{6})CGACTCACTACAGGG(.{6})TCGGTGACACGATCG(.{6})(.{6})/\1.2.4\4/g
		s/.*(.{6})CGACTCACTACAGGG(.{6})TCGGTGACACGATCG(.{6})(.{6})/\1\2\3\4/g
		n
		n
		s/.*(.{6}).{15}(.{6}).{15}(.{6})(.{6})$/\1.2.4\4/g
		s/.*(.{6}).{15}(.{6}).{15}(.{6})(.{6})$/\1\2\3\4/g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		done
		@@ -3295,7 +3296,7 @@ else
		s/^(.{9})CAGAGC(.{18})/T\1CAGAGC\2/g
		n
		n
		s/^(.{9})(.{6})(.{18})/F\1.2.4/g
		s/^(.{9})(.{6})(.{18})/F\1\2\3/g
		}' \|
		#remove linker (9 bp barcodes)
		sed -E '
		@@ -3439,10 +3440,10 @@ else
		#remove phase blocks and linkers
		sed -E '
		/.*(.{6})TAGCCATCGCATTGC(.{6})TACCTCTGAGCTGAA(.{6})ACG(.{8})GAC/ {
		s/.*(.{6})TAGCCATCGCATTGC(.{6})TACCTCTGAGCTGAA(.{6})ACG(.{8})GAC/\1.2.4\4/g
		s/.*(.{6})TAGCCATCGCATTGC(.{6})TACCTCTGAGCTGAA(.{6})ACG(.{8})GAC/\1\2\3\4/g
		n
		n
		s/.*(.{6}).{15}(.{6}).{15}(.{6}).{3}(.{8}).{3}/\1.2.4\4/g
		s/.*(.{6}).{15}(.{6}).{15}(.{6}).{3}(.{8}).{3}/\1\2\3\4/g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		done
		@@ -3457,10 +3458,10 @@ else
		#remove phase blocks and linkers
		sed -E '
		/.*CGAATGCTCTGGCCTTCGGACGATCATGGG(.{8})CAAGTATGCAGCGCGCTCAAGCACGTGGAT(.{8})AGTCGTACGCCGATGCGAAACATCGGCCAC(.{8})(.{10})$/ {
		s/.*CGAATGCTCTGGCCTTCGGACGATCATGGG(.{8})CAAGTATGCAGCGCGCTCAAGCACGTGGAT(.{8})AGTCGTACGCCGATGCGAAACATCGGCCAC(.{8})(.{10})$/\1.2.4\4/g
		s/.*CGAATGCTCTGGCCTTCGGACGATCATGGG(.{8})CAAGTATGCAGCGCGCTCAAGCACGTGGAT(.{8})AGTCGTACGCCGATGCGAAACATCGGCCAC(.{8})(.{10})$/\1\2\3\4/g
		n
		n
		s/.*.{30}(.{8}).{30}(.{8}).{30}(.{8})(.{10})$/\1.2.4\4/g
		s/.*.{30}(.{8}).{30}(.{8}).{30}(.{8})(.{10})$/\1\2\3\4/g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		#remove phase blocks and linkers (reverse complement if R2 matched)

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